Enabled & functioning edrfile reader.

pygmx/enxio.pyx

@@ -40,6 +40,7 @@ cdef extern from "gromacs/fileio/enxio.h":
 
     gmx_bool do_enx(ener_file_t ef, t_enxframe *fr)
 
+    void free_enxframe(t_enxframe *ef)
 
 
 cdef class EDRFile:
@@ -52,22 +53,45 @@ cdef class EDRFile:
 
     @property
     def types(self):
+
         types = []
         for i in range(self.n_etypes):
-            types.append(
-
-            )
-    def read(self):
-        cdef t_enxframe *frame
-        cdef np.ndarray[float, ndim=2] energies = np.empty((1,self.n_etypes), np.float32)
+            types.append((self.etypes[i].name.decode(), self.etypes[i].unit.decode()))
+        return types
 
+    def read(self, steps=None):
+        cdef:
+            t_enxframe *frame
+            np.ndarray[float, ndim=2] energies
+            np.ndarray[float, ndim=1] times
+        if steps is None:
+            energies = np.empty((1,self.n_etypes), np.float32)
+            times = np.empty((1,), np.float32)
+        else:
+            energies = np.empty((steps,self.n_etypes), np.float32)
+            times = np.empty((steps,), np.float32)
         snew(frame, 1)
 
-        while do_enx(self.efile, frame):
-            energies = np.resize(energies, (len(energies)+1, self.n_etypes))
-            for i in range(frame.nre):
-                energies[-1, i] = frame.ener[i].e
-        return energies
+        i = 0
+        while True:
+            cont = do_enx(self.efile, frame)
+
+            for j in range(frame.nre):
+                energies[i, j] = frame.ener[j].e
+            times[i] = frame.t
+
+            if cont:
+                i += 1
+                if len(energies) <= i:
+                    energies = np.resize(energies, (len(energies)+1, self.n_etypes))
+                    times = np.resize(times, (len(times)+1,))
+            else:
+                break
+
+        free_enxframe(frame)
+        sfree(frame)
+
+        return times, energies
 
 
     def __init__(self, filename):